Contacts of the strand formed by residues 75 - 81 (chain C) in PDB entry 2VTX
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 75 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20B GLY* 5.8 0.3 - - - -
64C GLU* 3.2 26.2 - - - +
65C ILE 3.6 2.8 + - - -
66C VAL* 3.9 8.8 - - - +
74C LYS* 1.3 73.7 - - - +
76C VAL* 1.3 59.8 + - - +
77C PRO* 3.6 9.0 - - - +
103C ARG* 3.1 26.5 + - - -
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Residues in contact with VAL 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ILE* 3.9 32.3 - - + +
19B TRP 3.6 11.9 - - - +
20B GLY* 3.7 27.4 - - - +
113B ILE 4.5 0.7 - - - +
114B SER* 3.5 32.5 - - - -
64C GLU* 3.2 3.3 - - - -
65C ILE 2.9 32.4 + - - +
74C LYS* 4.6 11.7 - - + +
75C SER* 1.3 74.1 - - - +
77C PRO* 1.3 71.3 - - + +
78C ILE* 3.5 4.8 - - + +
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Residues in contact with PRO 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B GLY* 6.2 0.2 - - - -
49B THR* 4.2 1.4 + - - -
51B CYS* 4.2 6.9 - - - -
112B TYR* 3.6 56.3 - - + +
113B ILE 5.1 0.2 - - - -
114B SER* 3.8 7.6 + - - -
62C ILE* 4.0 13.9 - - + -
63C VAL 3.8 1.3 - - - +
64C GLU* 3.6 25.1 - - + +
75C SER 3.6 10.1 - - - +
76C VAL* 1.3 93.5 - - + +
78C ILE* 1.3 61.0 + - - +
79C ALA 3.9 0.2 - - - -
105C LYS* 4.3 8.7 - - + +
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Residues in contact with ILE 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ILE* 4.9 2.0 - - + -
49B THR* 3.4 33.5 + - + +
51B CYS* 4.1 4.5 - - - -
88B MET* 3.8 3.8 - - - +
114B SER* 4.2 11.0 - - - +
47C LEU* 3.9 27.6 - - + -
50C VAL* 5.1 6.3 - - + -
63C VAL* 3.0 25.4 + - + +
65C ILE* 3.8 30.7 - - + -
76C VAL* 3.5 16.4 - - + +
77C PRO* 1.3 80.0 - - - +
79C ALA* 1.3 66.9 + - + +
91C MET* 4.3 14.0 - - - +
94C ILE* 4.5 11.7 - - + -
102C PHE* 5.1 1.8 - - + -
113C ILE* 5.9 0.9 - - + -
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Residues in contact with ALA 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B CYS* 4.0 2.0 - - - -
88B MET* 3.7 17.3 - - + -
50C VAL* 4.5 15.0 - - + -
61C HIS 4.3 0.2 - - - -
62C ILE* 3.3 8.5 - - - +
63C VAL* 3.1 43.3 + - + -
77C PRO 3.9 0.2 - - - -
78C ILE* 1.3 84.8 - - + +
80C THR* 1.3 63.3 + - - +
81C LEU* 4.3 5.8 - - + -
91C MET* 4.5 8.5 - - + -
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Residues in contact with THR 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B CYS* 3.3 18.1 - - - +
52B LEU* 2.7 31.4 + - + +
53B GLY 5.3 1.1 - - - -
87B PRO* 3.7 29.3 - - + +
88B MET* 3.3 27.1 - - - +
60C PHE* 3.9 26.5 - - + -
61C HIS 3.2 8.7 - - - +
62C ILE* 4.0 12.7 - - + +
79C ALA* 1.3 73.7 + - - +
81C LEU* 1.3 67.0 + - - +
86C LEU* 4.1 0.2 - - - +
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Residues in contact with LEU 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B PRO* 4.7 3.4 - - - -
88B MET* 4.0 4.7 - - - -
50C VAL* 3.7 33.2 - - + +
51C CYS* 4.3 0.2 - - - -
52C LEU* 3.9 26.0 - - + -
59C GLU 3.5 0.7 - - - +
60C PHE* 3.2 6.1 - - - -
61C HIS* 2.7 39.9 + - + +
79C ALA* 4.7 3.1 - - + -
80C THR* 1.3 89.5 - - - +
82C LYS* 1.3 61.7 + - - +
86C LEU* 3.2 14.6 - - + +
87C PRO 4.0 13.7 - - - +
88C MET* 3.5 31.2 - - - +
89C ALA* 3.7 12.3 - - + +
111C LEU* 4.7 4.0 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il